[BioC] problems running DEXseq

Simon Anders anders at embl.de
Sun Jun 30 21:14:48 CEST 2013

Hi Diya

On 29/06/13 01:32, Diya wrote:

> sudo samtools view ./Control_N1/Control_N1_thout/accepted_hits.sorted.bam |
> /data1/Bethsaida/python_scripts/dexseq_count.py -p yes
> HS.GRCh37.72_norm.DEXSeq.gff - combined.txt

Correct would be

sudo samtools view 
./Control_N1/Control_N1_thout/accepted_hits.sorted.bam | python 
/data1/Bethsaida/python_scripts/dexseq_count.py -p yes 
HS.GRCh37.72_norm.DEXSeq.gff - combined.txt

Before, you need to install HTSeq, as explained at

As Wolfgang already pointed out, your use of 'sudo' is very strange. I 
wonder if you might be following some incorrect instructions.


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